A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
Report
generated on 2024-04-15, 07:38 BST
based on data in:
/mnt/lustre/RDS-live/downing/LSDV_PVG/121_SAMPLE_PVG/CURRENT
ODGI
ODGI is an optimized dynamic graph/genome implementation, for efficient analysis and manipulation of pangenome graphs structured in the variation graph model.
Detailed ODGI stats table.
| Sample Name | Length | Nodes | Edges | Paths | Components | A | C | T | G | N |
|---|---|---|---|---|---|---|---|---|---|---|
| seqwish | 184251 | 6719 | 9126 | 13 | 1 | 59785 | 19693 | 58115 | 20645 | 26013 |
| smooth | 177727 | 7805 | 10640 | 13 | 1 | 58569 | 19182 | 56845 | 20117 | 23014 |
Sum of path node distances
For each path we iterate from node to node and count the node / nucleotide distance of nodes on the pangenome level normalized by the path length. If a node is reversed, we count the node distance twice.
This value allows you to evaluate the sorting goodness - how linear the graph is.
Mean links length
For each path we iterate from node to node and count the node / nucleotide distance mean_links_length
of nodes within the same path only. We then normalized by the path length.
This value allows you to evaluate the sorting goodness - how linear the graph is.
ODGI Compressed 1D visualization
This image shows a 1D rendering of the built pangenome graph. The graph nodes are arranged from left to right, forming the pangenome sequence. Summarization of path coverage across all paths. A heatmap color-coding from https://colorbrewer2.org/#type=diverging&scheme=RdBu&n=11 is used. Dark blue means highest coverage. Dark red means lowest coverage. The path names are placed on the left. The black lines under the paths are the links, which represent the graph topology.
ODGI 1D visualization
This image shows a 1D rendering of the built pangenome graph. The graph nodes are arranged from left to right, forming the pangenome sequence. The colored bars represent the paths versus the pangenome sequence in a binary matrix. The path names are placed on the left. The black lines under the paths are the links, which represent the graph topology.
ODGI 1D visualization by path position
This shows a 1D rendering of the built pangenome graph where the paths are colored according to their nucleotide position. Light grey means a low path position, black is the highest path position.
ODGI 1D visualization by path orientation
This image shows a 1D rendering of the built pangenome graph where the paths are colored by orientation. Forward is black, reverse is red.
ODGI 1D visualization by node depth
This shows a 1D rendering of the built pangenome graph where the paths are colored according to path depth. Using the Spectra color palette with 4 levels of path depths, white indicates no depth, while grey, red, and yellow indicate depth 1, 2, and greater than or equal to 3, respectively.
ODGI 1D visualization by uncalled bases
This shows a 1D rendering of the built pangenome graph where the paths are colored according to the coverage of uncalled bases. The lighter the green, the higher the 'N' content of a node is.
ODGI 2D drawing
This image shows a 2D rendering of the built pangenome graph.